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A study on the origin of plant-specific genes

English title A study on the origin of plant-specific genes
Applicant Wicker Thomas
Number 163325
Funding scheme Project funding (Div. I-III)
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Molecular Biology
Start/End 01.07.2016 - 30.04.2021
Approved amount 255'000.00
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Keywords (4)

Genome-wide analysis; Comparative genomics; Bioinformatics; Genome evolution

Lay Summary (German)

Lead
Eine der wichtigsten Fragen der Evolutionsbiologie ist, wie sich neue genetische Information entwickeln kann. Es war schon lange bekannt, dass sich viele evolutionäre Neuerungen durch Rekombination und “Wiederverwertung” von bereits existierenden Genen entwickeln. Manchmal jedoch scheinen Gene auch vollkommen neu aus genomischem “Rohmaterial” zu entsehen. In dieser Studie wir möchten die molekularen Mechanismen erforschen, die der Evolution von Genen und natürlicher Vielfalt zugrunde liegen.
Lay summary

Dank enormer Fortschritte in Sequenziertechnologien stehen uns heute die Sequenzen von tausenden von Genomen zur Verfügung. Mit grossangeleten vergleichenden Computeranalysen möchten wir Fälle identifizieren, wo neue genetische Information in einer Spezies oder einer Gruppe von meheren Spezies aufgetaucht ist. Wir werden uns zum einen auf die nahe verwandten Gräser Gerste und Weizen konzentrieren und versuchen, Gene zu identifizieren, die exklusiv nur in dieser Gruppe von Gräsern vorkommen. Andererseits werden wir auch weit entfernt verwandte Planzen vergleichen, und untersuchen, ob wir den Ursprung grosser Genfamilien zurückverfolgen können. Speziell möchten wir Fälle identifizieren, wo Gene durch horizontalen Transfer z.B. von Bakterien auf Pflanzen übetragen wurden. Diese Studien sollten es uns ermöglichen, zumindest einzelne molekulare Grundlagen und Prozesse zu identifizeiren, die sich hinter der Evolution genetischer Vielfalt und neuer Gene verbergen.

Direct link to Lay Summary Last update: 24.05.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat.
Kolodziej Markus C, Singla Jyoti, Sánchez-Martín Javier, Zbinden Helen, Šimková Hana, Karafiátová Miroslava, Doležel Jaroslav, Gronnier Julien, Poretti Manuel, Glauser Gaétan, Zhu Wangsheng, Köster Philipp, Zipfel Cyril, Wicker Thomas, Krattinger Simon G, Keller Beat (2021), A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat., in Nature communications, 12(1), 956-956.
Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen
PorettiManuel, PrazCoraline, MeileLukas, KälinCarol, SchaeferLuisa, SchläfliMichael, WidrigVictoria, Sanchez-ValletAndrea, WickerThomas, BourrasSalim (2020), Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen, in Mol Biol Evol, 37(3), 839-848.
A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew.
Müller Marion C, Praz Coraline R, Sotiropoulos Alexandros G, Menardo Fabrizio, Kunz Lukas, Schudel Seraina, Oberhänsli Simone, Poretti Manuel, Wehrli Andreas, Bourras Salim, Keller Beat, Wicker Thomas (2019), A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew., in The New phytologist, 221(4), 2176-2189.

Collaboration

Group / person Country
Types of collaboration
IPK Gatersleben Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Arizona Genomics Institute/University of Arizona United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Virtual 2020 Meeting on Repeat-Induced Point mutations Talk given at a conference Metagenomics of Cladonia lichens 19.10.2020 Zürich, Switzerland Wicker Thomas; Poretti Manuel Amos;
Plant and Animal Genome XXVIII Conference Poster Wheat Small RNA Response to Powdery Mildew Disease 11.01.2020 San Diego, United States of America Wicker Thomas; Poretti Manuel Amos;


Associated projects

Number Title Start Funding scheme
138504 A bioinformatics study to unravel molecular mechanisms that drive genome evolution 01.01.2012 Project funding (Div. I-III)

Abstract

Background:There are three main mechanisms that are thought to lead to the emergence of novel genes: (i) gene duplication that is followed by re-organization and/or neo-functionalization, (ii) horizontal gene transfer from a different taxonomic group and (iii) de novo evolution from non-coding DNA. In all three evolutionary paths, transposable elements (TEs) and/or double-strand break repair play a role. These events can nowadays be studied precisely by means of comparative genomics. Thus, with approriate genomic resources, evolution of new genes can be tracked and described both in a quantitative and a qualitative way. Working hypotheses:(i) Gene duplication is largely driven by DSB repair. (ii) Many major plant-specific gene families were acquired early on through horizontal gene transfer from bacteria or other prokaryotes. (iii) Genuine de novo gene evolution can be detected through comparative analysis of genes from closely related species. Experimental design:(i) Evolution of novel genes through duplication will be studied by searching closely related rice genomes for recent events of gene duplications or translocations. (ii) Horizontal gene transfer from prokaryotes to plants will be identfied through the search for prokaryotic homologs of all major plant gene families and through identification of sequences of bacterial origin in genes that were annotated as Triticeae-specific. (iii) We plan to compare so-called low-confidence genes from barely and wheat and submit them to vigorous selection criteria in order to distinguish genuine Triticeae-specific genes from annotation artifacts.
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